AMR/tests/testthat/test-eucast.R

39 lines
1.6 KiB
R
Raw Normal View History

context("eucast.R")
2018-03-27 17:43:42 +02:00
test_that("EUCAST rules work", {
2018-07-23 14:14:03 +02:00
expect_identical(colnames(septic_patients),
colnames(suppressWarnings(EUCAST_rules(septic_patients))))
2018-05-02 14:56:25 +02:00
2018-07-23 14:14:03 +02:00
a <- data.frame(bactid =
c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
2018-03-27 17:43:42 +02:00
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
2018-07-23 14:14:03 +02:00
b <- data.frame(bactid =
2018-07-26 16:30:42 +02:00
c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
"ENTAER"), # Enterobacter aerogenes
2018-03-27 17:43:42 +02:00
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
2018-07-23 14:14:03 +02:00
expect_identical(EUCAST_rules(a, info = FALSE), b)
expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
2018-04-02 16:05:09 +02:00
2018-07-23 14:14:03 +02:00
a <- data.frame(bactid =
c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
2018-03-27 17:43:42 +02:00
coli = "-", # Colistin
stringsAsFactors = FALSE)
2018-07-23 14:14:03 +02:00
b <- data.frame(bactid =
2018-07-26 16:30:42 +02:00
c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
2018-03-27 17:43:42 +02:00
coli = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(EUCAST_rules(a, info = FALSE), b)
})
test_that("MO properties work", {
expect_equal(mo_property("ESCCOL"), "Escherichia coli")
expect_equal(mo_property("STAAUR"), "Staphylococcus aureus")
})